I am working on a python script to extract couple of features from a text file.
The input file has following structure:
ENTRY M00001 Pathway Module
NAME Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate
CLASS Pathway modules; Carbohydrate metabolism; Central carbohydrate metabolism
PATHWAY map00010 Glycolysis / Gluconeogenesis
map01200 Carbon metabolism
map01100 Metabolic pathways
///
I am extracting value from 'ENTRY' field and 'PATHWAY' field. However, I am getting below as an output when I write the content to PostgreSQL 11.0 table.The column type is 'character varying'
id map_id
{M00001} {map00010,map01200,map01100}
{M00002} {map00010,map01200,map01230,map01100}
{M00003} {map00010,map00020,map01100}
{M00004} {map00030,map01200,map01100,map01120}
{M00005} {map00030,map00230,map01200,map01230,map01100}
Below code generate the above output:
cursor = conn.cursor()
dict = {}
with open ('file') as f:
for line in f:
if(re.search("^[A-Z]", line) ):
key, value = re.split("\s+", line, 1)
dict[key] = value
elif(re.search("^\s+", line)):
dict[key] = dict[key] + line
elif(re.search("^///", line)):
e = dict['ENTRY']
string = ''.join(e)
id = re.findall(r"(^[A-Za-z+]\d+)", string)
map_id = re.findall(r"(map\d+)\s+.*",dict['PATHWAY'])
cursor.execute("INSERT INTO tbl (id, map_id) VALUES (%s, %s)",(id, map_id))
conn.commit()
conn.close()
cursor.close()
The expected output is:
id map_id
M00001 map00010,map01200,map01100
M00002 map00010,map01200,map01230,map01100
M00003 map00010,map00020,map01100
M00004 map00030,map01200,map01100,map01120
M00005 map00030,map00230,map01200,map01230,map01100
Any help is highly appreciated